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Petra is in the desert, so rain is rare, but it's also in a dry river bed (wadi) so flash flooding after heavy rain is possible. It's worth noting this only affects the actual monument, the town of Petra where all the hotels etc are is located above the valley and is not subject to floods

So avoiding flash floods is simple enough: don't go into the valley after heavy rain upstream. (This applies to wadis anywhere, not just Petra.)